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When a flying saucer reportedly lands in rural Iowa, The Old Man (who runs a secret branch of the CIA), decides to investigate. He goes in person, accompanied by agents Sam (who is the son of The Old Man) and Jarvis, as well as Dr. Mary Sefton, a NASA specialist in alien biology. They find that aliens have indeed landed and are planning to use their mind-control powers to take over the Earth. The aliens are slug-like creatures, and they are attaching themselves to people's backs, taking control of their victims' nervous systems, and manipulating those people as puppets.

The slugs spread steadily, and soon attack one of the agents, Sam. Controlling Sam, aliens almost possess the president, too, but are defeated by the agents. Agents then learn they can remove a slug by an electric shock, and free Sam from the possession of a slug. It is soon found out all slugs share a common consciousness, a sort of a group mind.

The aliens quickly reproduce by division, soon controlling not only most of the population of the infested area, but also military personnel sent to the area to fight them.

As agents learn where the aliens' "hive" is located, they attempt to sneak in, and release Mary, whom aliens captured earlier. Together, they find surviving people whom slugs couldn't possess. They take one of them, a boy, with them, leaving the hive.

It is soon found out the boy suffered from encephalitis in the past, and that apparently was the reason a slug couldn't possess him. Biological warfare is adopted, and seemingly all parasites die. During a later inspection of a hive, The Old Man is attacked by the last healthy slug. In a fight on a helicopter, Sam destroys the parasite attached to the body of his father.

The screenplay went through a number of rewrites due to differences between the writers, Terry Rossio and Ted Elliott, who wanted to remain faithful to the Heinlein classic, and executives at Disney who wanted an adaptation that they could sell. As a result, the final script leaves out some elements of the novel, while portions of the movie follow the basic plot.[3]